30 December 2014

This is Albert Girther (left), held by Forrest Galante (right). This story is simultaneously cool and depressing. On the cool side, it’s wonderful to see such a charismatic beast. And I’m pleased to report this specimen was returned to the wild. It’s depressing because the story notes that lobsters of Albert’s size were once common. The big ones are rare now, thanks to fishing.

26 December 2014

Holidays are a time for opening things (like presents)! Today, I want share my latest experiences in open science, involving the recent paper I co-authored (Byrnes et al., 2014) about science crowdfunding and #SciFund. I was very pleased to see it land on the front page of PLOS ONE when it was released:

While I’ve been a supporter of open access, I have never quite gotten on board with what some have called “open notebook” science: posting the data as you go. For me, there are too many distractions and dead ends in an ongoing project. I would much rather wait until I have a complete story, all ready to be tied up in a bow in a published paper.

The #SciFund project, however, was much different. I got involved shortly after round one closed. I think it was the morning after it ended. Someone (for the life of me, can’t find it) posted an initial analysis of the round one projects: how much money they’d raised, donors, the project description length, and so on. I took that, gathered even more data, and shared it as a spreadsheet on Google Docs. Someone (Jarrett Byrnes, I think) then took that data, and archived it on Figshare.

I did the same after round two. And again on round three. And four. I stayed up quite late a couple of times so that I could collect the social media data (tweets and Facebook likes) from the Rockethub website as soon as the projects closed out. And I archived all that data, again, on Figshare.

So this time, all the data was public from the start.

Then, Jarrett and I blogged about what we were seeing in the data on the #SciFund blog. For instance, here’s one by me comparing the three rounds, and here’s one where Jarret admits that the model he developed to explain success in Round 1 didn’t explain success in Rounds 2 and 3:

(M)y first response was to freak out a little bit on the inside. I mean, have we been wrong this entire time? Have I been talking out of my scientific butt? Or did I get something deeply and fundamentally wrong.

The published paper reminded me of how long in the making this thing was. It was submitted in the middle of June 2012, and was published December 2014. This is the second time this year I’ve had a paper that took well over two years to make it to print. Unlike the first case, which was due mostly to delays on the editorial side, the journal and the authors both contributed to this delay. First, like the Southwestern Naturalist situation, the PLOS ONE editor initially handling the article went AWOL on us, and we had to find a new editor. Second, we authors were not always prompt making our revisions. Coordinating four authors can be tricky, and I can testify that we all worked on this thing. There are no gift authorships here!

After we had submitted the manuscript to PLOS ONE for review, we had a reasonably complete draft of the manuscript, and we submitted it as a pre-print to the PeerJ pre-print server.

What did I learn from this experience with doing the analysis out in the open?

Journal pre-publication peer review still matters

Plenty of people had chances to comment on our work, particularly after it was deposited in the PeerJ pre-print server. We did get comments on the pre-print, but the journal reviewers’ comments were more comprehensive.

Maybe we just got lucky with our reviewer. But, others have also expressed the opinion that people are most liable to act as peer reviewers when they are being asked to do it for a journal.

Publishing a peer-reviewed journal article still matters

By the time the PLOS ONE paper came out, I’d spent several years blogging about #SciFund here at NeuroDojo, on the #SciFund blog, and talking a lot about it on Twitter and other social media. The pre-print is very similar to the final published PLOS ONE paper. I worried nobody would pay an attention to the PLOS ONE paper, because there was not a lot there that we had not already talked about. A lot, I’d thought.

The word of mouth was helped by Jai organizing a press release through University of California Santa Barbara. (I tried to interest my university in putting out a press release. Silence from them.) That helped generate a reasonable number of pointers to this article on Twitter.

We also tried making a video abstract. It has a couple of hundred views now, which is not horrible.

And we did a panel discussion the week after the paper was released, too:

Following the panel discussion, the #SciFund paper rated an article on the Nature website.

But even among my regular followers, people who I thought might have looked at the pre-print, were commenting on the published paper. The pre-print didn’t get the traction that the final published paper did.

An excellent example of this is that we had one detailed comment picking apart Figure 8 in the PLOS ONE paper. Someone could have made this comment at the pre-print stage – this is one of the usual arguments for making pre-prints available. But the PLOS ONE comments feature isn’t used that often, so my reaction to the criticism was kind of summed up thus:

We’re still trying to figure out how to respond formally. Should we try to issue an erratum to the figure? Just post a corrected figure in the comments? But here is a new version of the figure:

Being open and sharing data is a good thing to do. But my experience with this paper suggests to me that the “screw journals” approach is not ready for prime time yet. And this was a project that, in theory, should have been a good one to try the “just blog it all as you go” method of sharing science. #SciFund was born and raised online. It exists because social media exists. I would have expected this paper to have reached its audience well before the final PLOS ONE paper came out. But all the blogging, tweeting, and pre-prints did not equal the impact of the actual journal article.

I am pleased this article is finally out. But we still have analysis from round four of #SciFund, and we are starting to eye round five, so I don’t think this will be my last crowdfunding paper.

23 December 2014

This was the scene last week, when H.E.B., a chain of grocery stores that runs through Texas and Mexico, donated a million dollars to the planned new UTRGV South Texas Diabetes & Obesity Institute.

It’s all very festive and season and everyone is playing off the Santa theme.

My reaction was more like this:

The H.E.B. donation creates a possible conflict of interest for UTRGV researchers.

Let’s start by stipulating that where money for research comes from matters. There is a large body of research on this. Ben Goldacre has documented a lot about the relationship between corporate funding and research results in his book, Bad Pharma. Here's a soundbite that is close to the bottom line (emphasis added):

(I)ndustry-funded trials are four times more likely to give a positive result than independently sponsored trials.

Given that the source of research funding can affect what results are ultimately published, what are possible problems here?

H.E.B. is part of the food industry. They don’t just distribute and sell other people’s food, either: they have their own in-house brands. This means they have vested interests in research results on diabetes and obesity. What they make, what they sell, and how their stores are laid out (their checkout isles are loaded with soft drinks and chocolate bars), all have implications both for their profitability and for public health, as this paper notes:

Retail food environments are considered influential in determining dietary behaviours and health outcomes.

On the surface, it’s hard to tell if this donation was made because H.E.B. wants to be on the right side of this issue, or whether it’s a public relations whitewash that is cheaper than actually changing their business practices in the service of public health.

Even if the donation was given in good faith, the H.E.B. donation may strongly influence the kind of research questions that the Institute can ask.

The South Texas Diabetes and Obesity Institute hasn’t published any research yet, but a research team has been recruited. It’s to be led by Sarah Williams-Blangero, whose CV lists her research interests as genetic epidemiology, infectious diseases (which diabetes is not), genetic management, and nonhuman primate genetics.

“Diabetes” and “obesity” are notable for their absence. In fact, out of over 100 publications listed on her CV, not one mentions “diabetes” or “obesity”in its title.

How interesting.

So what will the Diabetes and Obesity Institute publish research on? It isn’t clear yet, but it does not look good for someone who wanted to study the health impacts of certain kinds of food availability, social influences, advertising, and so on.

There have been cases like this before. American Academy of Family Physicians got sponsorship from Coca-Cola. The American Dietetic Association was criticized for accepting sponsorship from Hershey’s, the chocolate maker. This post on the latter mirrors my concerns:

I don’t doubt that the ADA has good intentions- they likely perceive sponsorships as potential to change corporate behaviors, working with them instead of against. But it is a huge conflict of interest, and there is a high risk that the companies will use the partnership to improve their image - here is Hershey already using it (and RDs) to tell the public that their chocolate products are ok - never-mind doses or which types, or the other ingredients that may come with it.

In an email, Travis Saunders (who blogs at Obesity Panacea) noted that the food industry often funds research related to obesity in some way (particularly exercise), but that there are no particular guidelines for health researchers in navigating the potential conflicts of interest. That there are no guidelines doesn’t mean everyone’s okay with this: there is contention among research in the area.

What would I like to see done about this? I am not saying that UTRGV should give back the money. First, I would like to see any research coming out of the Institute list the H.E.B. funding, and include it in their “conflict of interest” section in every paper and poster they publish.

Second, I want a real discussion about this among the university community. I find it a bit disturbing that they made this announcement in the week after final exams, when many students and faculty have already left campus, and there is not probably going to be much chance for discussion in university bodies like the faculty senate until late January.

UTPA and UTB were mainly teaching institutions, and did not get large amounts of research money. But as we transition to UTRGV, and to becoming a research university, we may need to give a lot more thought to what are acceptable funding sources and conflict of interest guidelines.

It’s not fun playing Grinch to this announcement, but maybe it is necessary. This may be more of a lump of coal than a gift.

Hard, because much obesity and diabetes research funded by food or pharma. Invited to collaborate on grant funded by Coke. Said no, but funding is limited. Sometimes it’s food and pharma money or no money at all.

Conflict of interest isn’t an all or nothing thing; there’s obviously gradations. I think the next question is, how do we manage these possible conflicts? I think full disclosure is a good first step.

18 December 2014

As an undergraduate, one of my professors recommended that you should study organisms that you like. In a new paper, Ferry and Shiffman talk about not getting that advice... in fact, they received advice that was about 180° away from it:

Scientists should not, according to this instructor while singling out DS and a student studying marine mammals as examples, pick a species that they “like” and then come up with a research question related to it. Author LF had a similar experience in graduate school, as she was also studying elasmobranchs. Both are/were perceived as “shark-huggers,” and felt pressure to defend their study organisms.

Ferry and Shiffman mention one common reason to study a particular organism: some are just convenient. It’s convenient for neurobiologists that squid have especially large axons, for instance. This is encapsulated as the Krogh principle, after physiologist August Krogh (pictured), who codified it thus:

For many problems there is an animal in which it can be most conveniently studied.

However, convenience is not, and should not, be the sole arbiter of species that people study. In fact, Krogh himself mentioned this, in the very same article (my emphasis):

I want to say a word for the study of comparative physiology also for its own sake. You will find in the lower animals mechanisms and adaptations of exquisite beauty and the most surprising character(.)

Every person picks what they study for their own reasons. It might be the organism, it might be the question, it might be something else. None of those many reasons reasons is inherently better than any other. To pick on someone for doing science than a different reason you do is pompous.

Small Pond Science looks at reference managers. Indispensable for any academic, in my opinion.

Jacquelyn Gill has become one of the latest in the online science community to have a crack at crowdfunding. She had one of the bigger successes I’ve seen, successfully raising over $10,000. She summarizes her experience here.

12 December 2014

We are always impressed by animals with large brains, because we have large brains. But, of course, even though we arguably show some of the greatest behavioural complexity, we don’t have the biggest brains, as this beautiful face reminds us.

Souzana Herculano-Houzel has proposed a simple hypothesis: the reason humans are as smart as we are is because we have more neurons than other animals.

What is it that we have that no other animal has? My answer is that we have the largest number of neurons in the cerebral cortex, and I think that’s the simplest explanation for our remarkable cognitive abilities.

“But we don’t have the biggest brains! Big animals have bigger brains! How can we have more neurons than they do?”

Herculano-Houzel has been investigating the scaling relationships between brain size and neuron number. The way brains get big differ in different groups of mammals (Herculano-Houzel 2009). In rodents, larger brains tend to have larger neurons. Primates follow different rules: larger brains tend to have neurons of about the same size.

This means that if you started with a rodent brain and a primate brain of the same size, and increased their volume by the same amount, the primate brain would get disproportionately more neurons.

This means that you can’t easily predict the brain size from one group of mammals using data from another group of mammals.

Herculano-Houzel and colleague recently published a pair of papers to test the “more neurons, more behavioural complexity” hypothesis using the elephant. First, Neves and colleagues (2014) examine the number of neurons in afrotherian mammals. The number of neurons in their brains scale with more like rodents than primates.

Although elephants are afrotherians, the analysis of their neuronal numbers comes in a separate paper (Herculano-Houzel et al., 2014). The total number of neurons in an African elephant’s brain is estimated to be three times greater than in humans (257 billion neurons compared to 86 billion)... but a huge proportion of those are in the cerebellum. And by huge, I’m talking about 97%.

The elephant’s cerebellum seems to be an outlier among mammals in several ways, but I’m not sure why. I’m not sure Herculano-Houzel or her colleagues know why, either. The “quick and dirty” function of the cerebellum in mammals is usually described as motor control, and maybe the distinctive trunk of elephants is playing an important role here.

How about the cortex, the centerpiece of Herculano-Houzel’s behavioural complexity hypothesis? An elephant’s cortex has about 5.6 billion neurons, compared to a human, which is estimated at around 16 billion.

This certainly seems consistent with her hypothesis, although I’m always a little wary of ascribing too much weight to the importance of the cortex. Karl Lashley spent a lot of time looking for the seat of memory in the cortex because people thought it must be important, and in so doing, overlooked the hippocampus in the formation of memory.

It would not surprise me in the slightest if Herculano-Houzel has whale brains in her lab awaiting analysis. Whales are the next obvious group to use these techniques with.

10 December 2014

As an organismal biologist, I like to imagine discovering a new species. In the course of researching a little departmental matter, I realized that our department can lay claim to introducing three new species to the world of science: a fish, a flower, and an insect.

09 December 2014

Watched a lot of Voyage to the Bottom of the Sea after school when I was very young. So much so that I don’t remember much of it besides my enjoyment, and thinking that the Seaview was one very cool design for a submarine. And alas, I don’t remember Victor Lundin’s protrayal of the title character of this episode:

These numbers show a higher education enterprise that is thriving, not in need of defense.

Yes, it’s true these data are only for science and engineering, but I have no reason to think those for other disciplines are dramatically different. Plus, when you read Napolitano’s comments, it’s pretty clear that she is mainly talking about economic competition in the scientific and engineering fields. For instance:

640 startups are based on inventions created within the University of California, she added(.)

And two of her three “grad school success stories” – success anecdotes, really – are about STEM disciplines (medical research and information technology).

And Napolitano trots out the hoary promise that huge numbers of academic jobs are going to open up:

(T)he state is projected to need tens of thousands of new professors as the baby boomer generation retires.

Yeah. I heard those projections before I started graduate school in the late 1980s. Yet somehow, over and over again, they never materialize. And let’s say the number of academic positions available per year in the United States doubles. Following the trend lines in the graph above, doctoral recipients are still going to outnumber faculty positions by three or four to one.

Napolitano is a politician with vested interests. It is in the interests of universities to lobby for more funding to support more graduate students. It is in the interests of universities to portray grad school and grad students as benefiting the greater good (which it does, by the way). And it is in the interests of universities to say that problems with a shortfall of employment opportunities are going to go away.

But Napolitano is lobbying for money, not defending something that is under threat in any meaningful way.

03 December 2014

Many are sharing this superb New York Times article on the woman who discovered the chemical francium. There are only just over 100 elements, and some were known to the ancients, so being the discoverer of a chemical element is a rare achievement indeed.

The article has a lot to offer. It’s part biography about one remarkable woman. It’s part indictment of scientific sexism of the past, lax attitudes about safety, and more. But I want to pull out this section near the end, which talks about science generally, which I liked a lot:

We should celebrate scientists not solely for their accomplishments but also for their courage and the tenacity required to discover anything at all. There are brave people out there working right now. They are brave not because they are killing themselves slowly or leaping from airplanes or catching rare tropical diseases, although scientists have done all those things. They are brave because of the intense emotional risks of trying to do something no one has done before by following your own lead. Radiation is a potent allegory for human life. Everything is always, inevitably falling apart; we are all in arrested decay. Our greatest achievements may become at best footnotes; few people remember us; we can’t know what will eventually come of our work.

01 December 2014

The old joke goes that places with terrible weather are made that way so only the best people live there. Dullards can’t hack it.

This little guy shows there may be some truth to that.

This is a black-capped chickadee (Poecile atricapillus). It’s a small bird that ranges over much of North America. Because it has such a wide distribution, the birds that live in different areas are slightly different from those that live in other areas. A recent paper by Kozlovsky and colleagues takes advantage of that to test an idea about brain size.

The expensive tissue hypothesis is an idea that says if you have more of one kind of expensive tissue (like brains), you will either have to:

Increase your overall metabolic rate to pay for the extra tissue.

Give up something. The original paper suggested that the gut was a prime candidate for reduction when brain size went up. It was also expensive, and you could compensate for a small digestive system with higher quality food.

A few papers have tested this, but this one is nice because it is all a single species. Kozlovsky and colleagues show nicely that the bigger the brain in the chickadee, the smaller the stomach and gut. This cleanly fits the expensive tissue hypothesis.

Heart size, on the other hand, does not correlate with brain size in any way. Again, this fits the original formulation of the expensive tissue hypothesis, which predicted that heart muscle would be unaffected by brain size. The need to pump blood kind of limits how much you can reduce heart tissue.

What was a little less expected was the influence the climate had on the birds.

The birds living in cold climates, like Fairbanks, Alaska (pictured) had bigger brains, and smaller bodies, than those living in more moderate, easy-going climes. Either one might be easy to explain on its own, but the combination is unexpected. Usually, both body size and brain size go up hand in hand (or, in this case, wing in wing). It’s not entirely clear how this is happening, although it certainly suggests there are some strong weather-related selection pressures shaping both features.

One factor that might be coming into play is that chickadees are food caching birds, and cold weather may actually allow the northern chickadees to store higher quality food for longer. The Alaskan chickadees live in a deep freeze, as it were, that lets them store insects and such for longer, because the cold weather means they don’t rot.